Báo cáo y học: "ESF-EMBO Symposium: Antiviral Applications of RNA Interference" pptx

BioMed Central
Page 1 of 7
(page number not for citation purposes)
Retrovirology
Open Access
Commentary
ESF-EMBO Symposium: Antiviral Applications of RNA Interference
Olivier ter Brake
†1
, Joost Haasnoot
†1
, Jens Kurreck
2
and Ben Berkhout*
1
Address:
1
Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA),
Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands and
2
Institute of Industrial Genetics,
University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
Email: Olivier ter Brake - ; Joost Haasnoot - ; Jens Kurreck - ;
Ben Berkhout* -
* Corresponding author †Equal contributors
Introduction
The first ESF-EMBO symposium on "Applications of anti-
viral RNA interference (RNAi)" was held in the spring of
2008 (5–10 april) in Sant Feliu de Guixols at the Costa
Brava in Spain. Some 60 participants from the fields of
RNAi research and virology came together to present their

latest findings on RNAi-virus interactions, as well as the
progress in the development of RNAi-based antiviral ther-
apeutics. One of the big topics concerned the role of RNAi
in natural antiviral defence mechanisms in mammals [1-
3]. In addition, new solutions to improve the efficacy and
safety of RNAi-based antiviral drugs were presented. The
combined expertise of researchers studying RNAi in
plants, insects and mammalian systems greatly stimulated
the overall discussion. The meeting was funded by the
European Science Foundation (ESF) in partnership with
the European Molecular Biology Organisation (EMBO).
RNAi in gene regulation and antiviral responses
RNAi is a post transcriptional gene silencing mechanism
that is triggered by double-stranded RNA (dsRNA). RNAi
and RNAi-related mechanisms play essential roles in the
regulation of cellular gene expression, as well as in innate
antiviral immune responses. As such, the importance of
RNAi in eukaryotic cell biology can hardly be overesti-
mated. In addition to its natural functions, RNAi as a tool
to specifically silence genes has in recent years revolution-
ized molecular biological research, and has provided new
possibilities in drug design [4]. Despite the fact that these
RNAi tools are now commonly used, still relatively little is
known about the natural functions of RNAi. So far the
role of RNAi in regulation of gene expression via endog-
enously expressed microRNAs (miRNAs) has received a
lot of attention [5]. miRNAs are small non-coding RNAs
that are expressed as long precursor RNAs (primary miR-
NAs) that are processed by the Drosha and Dicer enzymes
into a stem loop precursor miRNA (pre-miRNA) and the

mature miRNA (21–23 nucleotides), respectively. After
the mature miRNA is loaded into the RNA-induced silenc-
ing complex (RISC, sometimes referred to as miRISC), the
complex targets complementary sequences within the
3'UTR of a target messenger RNA, resulting in transla-
tional repression. It is currently estimated that expression
of at least 30% of all human genes is regulated by miRNAs
[6]. The exact criteria for target recognition are not clear.
However, pairing of the 5' 7–8 nucleotides of the miRNA
(seed region) to the 3' untranslated region of a target
mRNA is in many cases sufficient to trigger translational
inhibition [5-8].
The antiviral role of RNAi is well established in plants,
insects and nematodes [9]. In these organisms virus infec-
tion results in the production of virus-specific siRNAs that
target the viral RNA. These antiviral siRNAs arise from
dsRNA replication intermediates but have also been
shown to originate from sequences folding into extensive
secondary structures [10]. A cellular RNA-dependent RNA
polymerase is required for amplification of the siRNA sig-
nal and to trigger a potent antiviral RNAi response [11].
Plant and insect viruses counter the antiviral RNAi
response by expressing RNAi or silencing suppressor fac-
tors. At this meeting it again became clear that there is still
a lot of discussion about whether or not similar antiviral
RNAi responses play a role in mammals [1]. Similar to
Published: 18 September 2008
Retrovirology 2008, 5:81 doi:10.1186/1742-4690-5-81
Received: 4 July 2008
Accepted: 18 September 2008

This article is available from: />© 2008 ter Brake et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( />),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Retrovirology 2008, 5:81 />Page 2 of 7
(page number not for citation purposes)
plant and insect viruses several mammalian viruses have
been shown to encode factors that can inhibit RNAi, sug-
gesting repression by antiviral RNAi responses [12]. In
addition, cellular miRNAs have been shown to target viral
mRNAs [13-16]. However, so far virus specific siRNAs
could not be detected in virus infected mammalian cells.
Possibly, this is a technical issue. At the meeting it was
suggested that new deep sequencing technology may pro-
vide the sensitive tool that is required to identify virus spe-
cific siRNAs in mammalian cells.
RNAi technology
The first session of the meeting focused on RNAi technol-
ogy. The most common strategies to induce RNAi are sta-
ble intracellular expression of short hairpin RNA (shRNA)
or transient transfection of synthetic small interfering
RNAs (siRNAs). Mark Kay from Stanford University dis-
cussed RNAi-based gene therapy approaches against virus-
induced hepatitis using shRNAs. One of the problems of
this approach is that the adeno associated virus vector
used to deliver the shRNA-expression cassette can trigger
an immune response. To solve this problem one could
transiently suppress the immune response. However, a
more elegant method to evade immunity is to select for
less immunogenic vectors via capsid shuffling. This
approach resulted in a 100.000 fold more effective vector.

Another problem that was discussed was shRNA toxicity
[17]. Previously, it was shown that overexpression of
virus-specific shRNAs in liver caused lethality in mice by
saturation of Exportin 5 (Exp5), thus interfering with
export and maturation of endogenous microRNAs (miR-
NAs). New data was presented that also implicated Ago2,
the slicer in the RNA-induced silencing complex (RISC),
as a rate limiting factor. Combined overexpression of
Ago2 and Exp5 reduced toxicity associated with shRNA
overexpression and enhanced shRNA knockdown activity.
Focusing on the RNAi mechanism, Mark Kay and his co-
workers also asked the question why miRNA targets are
only functional in the 3'UTR of the mRNAs and not in the
open reading frame (ORF). Data was presented indicating
that miRNA translational inhibition is affected by the
speed of the translating ribosome. miRNA target
sequences within ORFs can in fact become functional
when translation is slowed down, e.g. when a miRNA tar-
get site is preceded by rare codons. Earlier, Lytle and co-
workers also showed functionality of miRNA targets in 5'-
UTRs of reporter genes, and concluded that any position
on a target RNA may be mechanistically sufficient to
repress translation [18].
Besides the use of viral vector systems for intracellular
expression of RNAi-inducers, synthetic siRNAs are also
considered highly effective candidate therapeutics.
Joachim Engels (Goethe University Frankfurt) gave some
background information about the chemical synthesis of
siRNAs. Developments like the 2'-acetoxyethyl (ACE)
RNA chemistry and the incorporation of modified, espe-

cially cationic, nucleotides form the basis for the synthesis
of highly stable effective siRNAs. Jorgen Kjems (University
of Aarhus) discussed some of the latest developments in
the use of modified siRNAs. One of the major problems
with synthetic siRNAs is their low stability in serum. A
comprehensive study was conducted with many different
chemistries at the 2'O ribose position such as aminoethyl
and guanidinoethyl [19], and it was shown that siRNA
half life and efficacy can be greatly enhanced by introduc-
ing modifications at specific positions both in the passen-
ger and the guide strand of the siRNA. Off-target effects
caused by the incorporation of the passenger strand in
RISC were effectively avoided by design of a nicked pas-
senger strand in the so called small internally segmented
interfering RNA (sisiRNA) design. Furthermore, off-target
effects could be avoided by incorporation of specific mod-
ifications in the guide strand of the siRNA. In addition,
Kjems focussed on siRNA delivery systems and showed
that nanoparticles based on chitosan were highly effective
for siRNA delivery, particularly in the lungs.
An interesting novel technique termed RNAu was pre-
sented by Puri Fortes (University of Navarra) [20]. RNAu
is based on expression of U1 small nuclear RNA (snRNA)
of which the 5' nucleotides 2–11 are modified to base-pair
with a 10 nucleotide target within the 3' terminal exon of
a gene of interest. Binding of the modified U1 snRNA
inhibits polyadenylation, resulting in degradation of the
transcript and gene knockdown. The U1 snRNA mecha-
nism tolerates a single mismatch at positions 1, 2, 9 and
10, the central 6 nucleotides require perfect base-pairing

but do allow a single G-U base-pair. The presence of mul-
tiple target sites within the 3' exon enhances inhibition,
and a knockdown of gene expression of up to 700-fold
can be achieved. Interestingly, when combined with
RNAi, additive or even synergistic inhibition was
obtained.
Plants viruses and RNAi
Thomas Hohn (University of Basel) introduced the mech-
anism of RNAi in plants and its interaction with viruses.
Plants use RNAi as an antiviral defence in which viral rep-
lication intermediates in the form of dsRNA are processed
by the Dicer-like enzyme (DCL) [9]. Furthermore, plants
can amplify the RNAi effect using RNA-dependent RNA
polymerase (RdRP) and siRNAs as primers. The RNAi
machinery in plants is rather complex with four DCL
enzymes: DCL1 processes primary-miRNA (pri-miRNAs)
with different product sizes depending on the substrate,
DCL2-4 process dsRNA. DCL2 can compensate for defi-
ciencies in the other DCL enzymes and yields a 22-nucle-
otide (nt) product, DCL3 and 4 produce 24 and 21-nt
Retrovirology 2008, 5:81 />Page 3 of 7
(page number not for citation purposes)
siRNAs, respectively. RNAi in plants can be triggered by
DNA viruses and RNA viruses. For instance, Hohn showed
that two DNA viruses, the Cabbage leaf curl virus (CaL-
CuV) and the Cauliflower mosaic virus (CaMV), triggered
the synthesis of 21, 22 and 24-nt siRNAs, and the cyto-
plasmic RNA tobamovirus Oilseed rape mosaic virus
(ORMV) triggered predominantly 21-nt siRNAs. Since the
RNAi machinery in plants can act as a potent antiviral

response, viruses in turn have evolved RNA silencing sup-
pressors (RSS) as a countermeasure. For instance, the p19
protein from Tombusvirus can bind and neutralize siR-
NAs. Interestingly, the AC2 protein from Mungbean yel-
low mosaic virus-Vigna (MYMV) is not an RNAi
suppressor itself, but apparently triggers the activation of
an endogenous RSS activity.
Björn Krenz (University of Stuttgart) reported on the Abu-
tilon Mosaic Virus, which was engineered as a versatile
vector to deliver genes in to plants. It was subsequently
employed to silence phytoene desaturase in Nicotiana
benthamiana, demonstrating that this viral vector is a val-
uable tool for functional studies. Juan Antonio García
(CNB-CSIC, Madrid) presented work on the cucumber
vein yellowing Virus (CVYV), which is a member of the
potyviridae. Remarkably, CVYV does not encode the
silencing suppressor HCPro that is typical for potyviridae,
but instead produces the P1a-b protein that is proteolyti-
cally processed into P1a and P1b instead of a single P1
protein. P1b is a serine protease that accumulates in
infected plants and functions as an RSS. It contains a Zn-
finger and LXKA basic motif, which are both required for
RSS function. P1b binds siRNAs but also endogenous
miRNAs, which affects the miRNA expression pattern of
the host cell. In the plum pox virus, HCPro could be
replaced by P1b, adding further proof that P1b is an RSS.
Kirsi Lehto (University of Turku) presented data on plant
virus encoded RSS factors and their role in virus-induced
disease. RSS genes derived from six virus genera were
transformed into Nicotiana benthamiana and N. tabacum

plants. Depending on the species of the host plant the
RNA silencing suppressors caused different disease phe-
notypes. In addition, the suppressors demonstrated differ-
ent effects on crucifer-infecting Tobamovirus (crTMV)
infections. Apparently, these suppressors act at different
levels in the RNAi pathway, and interfere with miRNA
function to variable degrees.
Olivier Voinnet (Institute de Biologie Moléculaire des
Plantes, Strasbourg) showed that the interaction between
host and pathogen is more complicated than simple
defence and counterdefence mechanisms. Arabidopsis
encodes for 10 different Ago genes, Ago1 minus plants are
hypersensitive to viruses indicating that Ago1 is involved
in antiviral responses. Previously, Ago1 was shown to act
within the miRNA pathway. Thus, miRNA and antiviral
pathways appear to converge. In addition to RNA silenc-
ing, resistance (R) genes are also involved in blocking
virus replication in plants. These genes encode receptors
that detect pathogens and activate strong defences similar
to pattern-recognition receptors in mammals [21]. It is
becoming clear that genes involved in RNAi are in fact R
genes that regulate the hypersensitive response (HR). HR
causes apoptosis of the local region surrounding the infec-
tion thus preventing further viral spread. There is also evi-
dence that HR factors are part of RISC. Although the
antiviral function of RNAi in mammals is still debated,
Olivier Voinnet extended the function of RNAi in plants
to a defence against bacterial pathogens [22,23]. Specific
plant miRNAs are induced in response to bacterial patho-
gens that are detected via the flagellin receptor. Similar to

viruses, bacteria also encode specific factors that are trans-
located to the plant cells to block the miRNA pathway.
These effectors were identified and found to affect
processing of Ago1. In this way, viral and bacterial infec-
tions can join forces and benefit from each others pres-
ence by a severe attack on the RNAi defence mechanism.
Drosophila and innate antiviral responses
In this session the focus was on RNAi mechanisms in Dro-
sophila and their interaction with viruses. Drosophila
encodes two Dicer enzymes, Dcr1 is involved in miRNA
processing and Dcr2 processes dsRNA into siRNAs. The
RNAi mechanism acts as a potent innate response against
viral infection. Ronald van Rij (Radboud University
Nijmegen) presented data highlighting the antiviral role
of RNAi in insect cells by showing that Ago2-minus Dro-
sophila melanogaster exhibit increased susceptibility to
Drosophila C virus (DCV) infection and that the virus
encodes an RSS. Using Sindbis virus, which can infect
both mammalian and insect cells, it was shown that
knockdown of Ago2 and Dcr2 in insect cells increased
virus production, whereas knockout of Dcr in mouse cells
had no effect. These results suggest that RNAi has no role
in the mammalian antiviral defence against Sindbis virus.
Jean-Luc Imler (Université de Strasbourg) also showed
that RNAi is an antiviral response mechanism in insects.
He demonstrated that Dcr2-minus cells are more sensitive
to Flock house virus (FHV) and that the B2 protein is an
RSS that binds dsRNA. More importantly, he presented
interesting work suggesting that the virus-specific RNAi
response triggers a secondary antiviral response involving

JAK/STAT signalling and the production of cytokines. A
key factor in this cellular response pathway is Vago, whose
induction is also suppressed by the FHV B2 protein, indi-
cating that dsRNA triggers the inducible antiviral
response.
Retrovirology 2008, 5:81 />Page 4 of 7
(page number not for citation purposes)
Carla Saleh (Institute Pasteur, Paris) presented data on the
spread of the RNAi signal to neighboring cells. In plants,
systemic spread of the antiviral RNAi signal is important
for viral clearance. Similar mechanisms were thus far not
observed in flies. Insect cells do not take up siRNAs, but
they can take up large dsRNA molecules that subsequently
induce RNAi. Cellular factors involved in this RNA-uptake
were identified and knockout mutant flies were shown to
be hypersensitive to viral infection by Sindbis and DCV.
Virus-induced cell lysis results in release and spread of
virus-specific dsRNA molecules that are taken up by unin-
fected surrounding cells, thus generating an antiviral state.
Interactions between mammalian viruses and
cellular RNAi mechanisms
Recently, it has become clear that mammalian viruses
interact with components of the host RNAi machinery.
Viruses can express miRNAs to regulate the expression of
cellular genes, or viral gene expression may be activated or
repressed by cellular miRNAs. In addition, several viruses
encode suppressors of RNAi. A separate session was dedi-
cated to these complex interactions between viruses and
the RNAi machinery.
Goran Akusjarvi (Uppsala University) presented data on

how adenovirus interacts with the RNAi/miRNA path-
ways. He showed that the structured non-coding virus-
associated RNAs (VA RNA I and II) are processed by Dicer
and incorporated into RISC. Although only 2–5% of the
total amount of the VA RNAs is diced, up to 80% of all
RISC complexes contain VA-derived si/miRNAs late in
infection [24]. Of these, ~80% stem from VA RNAII,
which is expressed at much lower levels than VA RNAI.
Besides this VA RNAII bias, there also appears to be a
strand bias for incorporation into RISC. Data was pre-
sented that this bias may arise from two different tran-
scription initiation sites that are used during VA RNA
expression. Puri Fortes (University of Navarra) presented
data that blocking of the adenoviral VA miRNAs results in
a decrease in viral titer, suggesting that VA miRNAs con-
trol the expression of genes whose expression affects ade-
novirus production. This group has also identified several
putative targets for these miRNAs using a combination of
bioinformatic approaches and microarray analysis. How
these targets affect the viral cycle remains to be estab-
lished.
Does RNAi play a role in antiviral immune
responses in mammals?
One of the most fiercely discussed issues during the meet-
ing was the question whether or not RNAi has a role in
antiviral mechanisms in mammals. On the one hand, it
has been shown that several mammalian viruses encode
RSS functions, implying that the virus must have evolved
this functionality in order to suppress RNAi [12]. On the
other hand, virus-specific siRNAs could thus far not be

detected in virus-infected mammalian cells, which is
unlike the situation in plant and insect cells. Bryan Cullen
(Duke University) started the discussion by summarizing
data that do not support a role for antiviral RNAi
responses in mammals. For example, long dsRNA induces
the interferon (IFN) response in mammalian cells
whereas these molecules trigger a potent and specific
RNAi response in plants and insects. Furthermore, human
immunodeficiency virus type 1 (HIV-1) infection does
not result in the production of virus-specific siRNAs. The
reported RNAi suppression activity of the HIV-1 Tat pro-
tein and the primate foamy virus type 1 (PVF-1) Tas pro-
tein was claimed to result from promoter activation rather
than RNAi suppression. For example, the Tat-induced
increase in expression of a shRNA silenced reporter would
result from activation of the promoter controlling firefly
expression instead of blocking the shRNA-induced RNAi
response. Cullen concluded that mammalian viruses nei-
ther induce nor repress siRNAs because there is no need to
do so. Instead, mammalian viruses use the RNAi pathway
for their own benefit by expression of virus-encoded miR-
NAs that target cellular mRNAs. Cullen showed that the
Herpes simplex virus type 1 (HSV-1) expresses several
miRNAs from the LAT-gene that target viral immediate
early mRNAs. These miRNAs did not include the miR-LAT
that was previously reported. Interestingly, the viral miR-
NAs trigger inhibition of translation despite the fact that
the mRNA target is located within the ORF sequences.
The discussion on the role of RNAi in mammals was con-
tinued by Kuan-Teh Jeang (National Institutes of Health,

USA) who summarized literature data that favour the anti-
viral role of RNAi in mammals [25]. In addition, he pre-
sented preliminary results from deep-sequencing analysis
of small RNAs from HIV-1 infected cells. In total, 163
clones of several small virus-specific RNAs were detected.
It is currently unclear whether these are incorporated into
RISC and thus represent antiviral siRNAs. It also needs to
be excluded that these small RNAs merely represent
degraded RNA, although the discrete size range of these
RNAs suggests that this is not the case. Besides these de
novo produced virus specific small RNAs, several groups
have recently shown that cellular miRNAs can also target
and inhibit the expression of viral mRNAs. However, the
physiological significance of such a mechanism is debated
because it appears paradoxical for the virus to retain func-
tional miRNA target sites in their RNA genome. Possibly,
the virus benefits from downregulation by miRNAs.
Fatah Kashanchi (George Washington University) pre-
sented data suggesting that the TAR hairpin at the 5' end
of HIV-1 transcripts is recognized by Dicer and processed
into functional miRNAs. The amount of TAR miRNAs pro-
duced seems to vary significantly between different HIV-1
Retrovirology 2008, 5:81 />Page 5 of 7
(page number not for citation purposes)
infected cell lines. In the absence of Tat protein, these
short transcripts appear to be extremely abundant both in
cell lines and latent primary infected cells. This suggests
that perhaps the TAR miRNA is involved in transcriptional
silencing of the integrated proviral DNA genome, thereby
contributing to latency. Finally, in a recent collaboration

with the group of Zvi Bentwich (Rosetta Genomincs Ltd.,
Israel), they have been able to clone the TAR miRNAs
from infected cells.
Monsef Benkirane (Institute de Genetique Humaine,
Montpellier) showed that knockdown of Drosha, Dicer
and DGCR8 in mammalian cells resulted in increased
HIV-1 production, which was linked to the previously
reported role of miRNAs in maintenance of HIV-1 latency
[13]. However, Anne Gatignol (McGill University, Mon-
treal) showed that knockdown of TRBP and Dicer resulted
in a decrease in virus production. These results appear to
be contradictory but may arise from specific differences in
experimental set up. Enhancers and repressors of virus
replication may both be regulated by miRNAs. Knock-
down of the RNAi pathway may therefore go either way.
Previously, Huang and co-workers showed that cellular
miRNAs are involved in the control/maintenance of
latency [13]. It was suggested that these miRNAs may rep-
resent new antiviral drug targets. Inhibition of these spe-
cific latency miRNAs would result in activation of latent
virus reservoirs that are normally difficult to target with
highly active antiretroviral therapy (HAART). Activation
of the HIV-1 reservoirs would allow recognition and elim-
ination of all infected cells by the immune system.
Joost Haasnoot (University of Amsterdam) also presented
data on the interplay of cellular miRNAs and HIV-1 repli-
cation. miRNA expression profiles were studied in HIV-1
infected T-cells using a quantitative RT-PCR approach. In
HIV-1 producing cells, 11 out of a total of 293 studied
miRNAs were significantly affected. A bioinformatics

analysis indicated that 8 of these 11 miRNAs have poten-
tial target sites within the HIV-1 genome. These miRNAs
add to the current list of candidate miRNAs that target
HIV-1. Interestingly, these new targets cluster to specific
regions of the HIV-1 genome, suggesting a positive selec-
tion during virus evolution. Anne Gatignol addressed
whether viruses inhibit the endogenous RNA silencing
pathways, e.g. by means of a suppressor protein. Whereas
HIV-1 did not inhibit RNAi-mediated knockdown in cells
transfected with exogenous shRNAs, such an inhibition
was exerted by the virus on cell endogenous miRNAs that
target perfecty complementary sites in a reporter gene.
HIV-1 RNAi therapeutics
A major problem with antiviral approaches against HIV-1
is the emergence of escape variants. Similar to the emer-
gence of drug resistant mutations, RNAi resistant muta-
tions have also been described [4]. Thus, for the
development of effective RNAi-based therapies against
escape-prone viruses, the main objective is to effectively
suppress virus replication while preventing the selection
of resistant variants. In case of HIV-1 this is further com-
plicated by the large heterogeneity of viral sequences
within a patient. Miguel Angel Martinez (irsiCAixa Foun-
dation, Barcelona) described two approaches aimed at
preventing viral escape. First, one could counteract escape
mutations against a specific siRNA by including second
generation siRNAs that are directed against these specific
mutants. In addition, one could also inhibit the virus with
multiple siRNAs generated in vitro from Dicer-cleaved
long dsRNA.

Karin Metzner (University of Erlangen) addressed the
problem of HIV-1 resistance against regular antiviral
drugs. It was proposed to use RNAi to specifically suppress
these escape variants. Combining 3TC, a nucleoside
Reverse Transcriptase inhibitor, with an siRNA directed
against the most common 3TC-resistance mutation
(Met184Val), proved to be effective in cell culture infec-
tions. Targeting essential cellular co-factors could be a
valid approach to avoid RNAi resistance but also a way of
defining new therapeutic targets. Eduardo Pauls (irsiCaixa
Foundation, Barcelona) showed that targeting of αV
integrin and β5 integrin with siRNAs could inhibit HIV-1
replication. This inhibition was not at the level of virus
entry, reverse transcription or integration but appeared to
block transcription from the HIV-1 long terminal repeat
promoter. However, siRNAs were used in all of the above-
mentioned approaches, and siRNA delivery in patients is
still a major bottleneck.
Olivier ter Brake (University of Amsterdam) presented
results on the development of an RNAi-based gene ther-
apy for HIV-1. A single treatment with a lentiviral vector
expressing a single shRNA results in stable induction of
RNAi. In a combinatorial approach, four antiviral shRNAs
were expressed from a single lentiviral vector. In a T cell
line containing a single vector copy per cell, HIV-1 repli-
cation could be effectively controlled for up to 40 days,
while escape mutants emerged in control single shRNA
cell lines. This result highlights the therapeutic potential
of such an approach. However, safety aspects still require
intensive investigation. A pilot study was performed in a

humanized mouse model in which Rag2
-/-
γ
c
-/-
irradiated
newborn mice are engrafted with shRNA-transduced
human haematopoietic stem cells. Development of the
immune system was not affected by constitutive shRNA
expression, although a slightly reduced engraftment effi-
ciency of the transduced cells was observed. Furthermore,
sequence-specific inhibition of HIV-1 replication was
demonstrated in CD4+ T cells from this mouse [26].
Retrovirology 2008, 5:81 />Page 6 of 7
(page number not for citation purposes)
Combining antiviral RNAi with immune
stimulation
Hepatitis C virus (HCV) virus infection is a major cause of
chronic liver disease with nearly 200 million carriers
worldwide. The current standard treatment with
pegylated-interferon-alpha (IFN-α) administered in com-
bination with Ribavirin is only effective in half of the
patients, prompting the need for alternative therapies.
RNAi represents an attractive new approach against HCV,
allowing knock-down of viral RNA or host factors
involved in the virus life cycle. Based on their distinct anti-
viral mechanism, Qiuwei Pan (Erasmus University, Rot-
terdam) proposed that combining lentiviral vector
mediated RNAi with IFN-α treatment may avoid thera-
peutic resistance and exhibit enhanced antiviral activity.

However, there is some concern about a potential nega-
tive effect of IFN-α on vector transduction, but such an
effect was not observed. Gunter Hartman (University of
Bonn) presented his research at the interface of RNAi and
interferon responses. Most researchers try to avoid siRNA
side-effects. Instead, Hartman proposed to design siRNA
specifically for immunorecognition and to use this addi-
tional activity for therapy. Such siRNA not only induce
RNAi, but also TLR7 and RIG-I by inclusion of appropriate
TLR7 motifs (5'-GUCCUUCAA-3', 5'-UGUGU-3' and
derivatives thereof [27,28]), and 5'-triphosphates. Such
an approach can be advantageous against viral infections
and cancer.
Cocksackie B3 and other viruses
Jens Kurreck (University of Stuttgart) presented data on
RNAi-mediated inhibition of Coxsackie B3 virus (CoxB3).
Using reporter constructs and virus he showed that only
the plus-stranded RNAs can be targeted by the siRNAs. In
addition, Kurreck showed that it is difficult to induce effi-
cient RNAi knockdown when viral sequences are targeted
that have complex RNA secondary structures.
Rainer Wessely (Munich University of Technology) gave
an overview of CoxB3 involved in viral heart disease. siR-
NAs against CoxB3 were effective both in vitro and in an in
vivo mouse model, yielding a 2–3 log reduction in virus
replication. However, virus resistance was observed
already after the first infection cycle, indicating that com-
binatorial RNAi approaches are required for effective and
durable suppression. In an alternative approach, Sandra
Pinkert (Charité, Berlin) demonstrated that CoxB3 can

efficiently be inhibited in neonatal rat cardiomyocytes by
vector mediated delivery of shRNA expression cassettes
against the virus genome or its receptor, the coxsackievi-
rus-adenovirus receptor (CAR). A soluble variant of CAR
fused to the Fc domain of a human immunoglobulin had
an even more potent antiviral effect suggesting that it
might be worth to combine the different approaches.
Carolyn Coyne (University of Pittsburgh) uses RNAi to
investigate entry of enteroviruses into polarized endothe-
lial cells. Recently, she used a large scale screen to identify
genes involved in entry of CoxB3 and poliovirus. One of
the hits, the Yes kinase was characterized in more detail by
low molecular weight inhibitors and its knockdown or
inhibition was found to prevent entry of CoxB3 (but not
of poliovirus) into human bone marrow endothelial cells.
Alexander Karlas (Max-Planck-Institute for Infection Biol-
ogy, Berlin) reported on the use of RNAi against influenza
virus A. siRNAs modified with locked nucleic acids (LNA)
and delivered by chitosan were found to be efficient in a
mouse influenza model. In order to identify host factors
on which the virus depends large scale screens were per-
formed and a large number of factors from the spliceo-
some were among the hits.
Towards clinical applications
Jörg Kaufmann (Silence Therapeutics AG, Berlin) pre-
sented data on Atu027, an anti-cancer siRNA delivered
systemically for the treatment of gastrointestinal cancer.
Although not an antiviral RNAi approach, this presenta-
tion nicely listed the challenges of the clinical develop-
ment of RNAi therapeutics. First of all, a formulation was

developed, Atuplex, which consists of liposomes of ~120
nm containing a cationic lipid and a helper-lipid PEG-
lipid, in which the siRNA is incorporated, a blunt ended
23-mer with 2'-O-methyl modification for stabilisation.
The complex could be lyophilized and stored long-term at
4°C without significant loss of efficacy, an important
requirement for clinical development. Furthermore, bio-
distribution, toxicology and efficacy studies were con-
ducted in various animal models. The siRNA was found
mostly in the endothelial cells of the lung but did not pen-
etrate the tumor. No cytokines were induced, indicating
that siRNA administration is safe. Furthermore, metastasis
was reduced in a prostate cancer model. Combined, the
data showed that Atu027 is effective and safe. Currently,
Silence Therapeutics is preparing for a phase I clinical trial
that is expected to start this year.
Concluding remarks
In light of the new data presented at this meeting it is
clearly too early to close the door on an antiviral function
of RNAi in mammals. Instead, data in favour of an antivi-
ral role of RNAi in mammals are accumulating. In addi-
tion, viruses and the cellular RNAi machinery interact in
multiple different ways. This meeting has shown that both
fundamental research on RNAi and viruses and the appli-
cations of RNAi technology are developing fast. An impor-
tant discussion point during the meeting was about the
future for RNAi therapeutics [29]. RNAi can be very potent
and specific, underscoring the great potential of this
mechanism. However, increasing concerns about toxicity
Publish with BioMed Central and every

scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
/>BioMedcentral
Retrovirology 2008, 5:81 />Page 7 of 7
(page number not for citation purposes)
and off-target effects have tempered these initial expecta-
tion for a rapid introduction of RNAi-based drugs in the
clinic. Despite these concerns, pharmaceutic companies
are investing in the further development of RNAi-based
therapeutics. Currently, it is safe to say that we have only
a limited understanding of the RNAi pathway and its func-
tions. A more thorough understanding will contribute to
the fine-tuning of RNAi-based drugs such that safe and
effective RNAi based therapeutics can be developed.
Acknowledgements
We thank Y.P. Liu for her advice and suggestions during preparation of the
manuscript. The meeting was made possible by support of the ESF in part-
nership with the European Molecular Biology Organisation (EMBO). RNAi
research in the Berkhout lab is sponsored by ZonMw (Vici grant and Trans-
lational Gene Therapy program), NWO-CW (Top grant), the European
Union (LSHP-CT-2006-037301) and the Technology Foundation STW
(grant AGT.7708).

References
1. Cullen BR: Is RNA interference involved in intrinsic antiviral
immunity in mammals? Nat Immunol 2006, 7:563-567.
2. de Vries W, Haasnoot J, van dV, van Montfort T, Zorgdrager F, Pax-
ton W, Cornelissen M, van Kuppeveld F, de Haan P, Berkhout B:
Increased virus replication in mammalian cells by blocking
intracellular innate defense responses. Gene Ther 2008,
15:545-552.
3. Yeung ML, Benkirane M, Jeang KT: Small non-coding RNAs,
mammalian cells, and viruses: regulatory interactions? Retro-
virology 2007, 4:74.
4. Haasnoot J, Westerhout EM, Berkhout B: RNA interference
against viruses: strike and counterstrike. Nat Biotechnol 2007,
25:1435-1443.
5. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel
DP: MicroRNA targeting specificity in mammals: determi-
nants beyond seed pairing. Mol Cell 2007, 27:91-105.
6. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMe-
namin P, da PI, Gunsalus KC, Stoffel M, Rajewsky N: Combinatorial
microRNA target predictions. Nat Genet 2005, 37:495-500.
7. Brennecke J, Stark A, Russell RB, Cohen SM: Principles of micro-
RNA-target recognition. PLoS Biol 2005, 3:e85.
8. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB: Predic-
tion of mammalian microRNA targets. Cell 2003, 115:787-798.
9. Ding SW, Voinnet O: Antiviral immunity directed by small
RNAs. Cell 2007, 130:413-426.
10. Molnar A, Csorba T, Lakatos L, Varallyay E, Lacomme C, Burgyan J:
Plant virus-derived small interfering RNAs originate pre-
dominantly from highly structured single-stranded viral
RNAs. J Virol 2005, 79:7812-7818.

11. Wassenegger M, Krczal G: Nomenclature and functions of
RNA-directed RNA polymerases. Trends Plant Sci 2006,
11:142-151.
12. de Vries W, Berkhout B: RNAi suppressors encoded by patho-
genic human viruses.
Int J Biochem Cell Biol 2008, 40:2007-2012.
13. Huang J, Wang F, Argyris E, Chen K, Liang Z, Tian H, Huang W,
Squires K, Verlinghieri G, Zhang H: Cellular microRNAs contrib-
ute to HIV-1 latency in resting primary CD4(+) T lym-
phocytes. Nat Med 2007, 13:1241-1247.
14. Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber
C, Saib A, Voinnet O: A cellular microRNA mediates antiviral
defense in human cells. Science 2005, 308:557-560.
15. Otsuka M, Jing Q, Georgel P, New L, Chen J, Mols J, Kang YJ, Jiang Z,
Du X, Cook R, Das SC, Pattnaik AK, Beutler B, Han J: Hypersuscep-
tibility to vesicular stomatitis virus infection in Dicer1-defi-
cient mice is due to impaired miR24 and miR93 expression.
Immunity 2007, 27:123-134.
16. Triboulet R, Mari B, Lin YL, Chable-Bessia C, Bennasser Y, Lebrigand
K, Cardinaud B, Maurin T, Barbry P, Baillat V, Reynes J, Corbeau P,
Jeang KT, Benkirane M: Suppression of microRNA-silencing
pathway by HIV-1 during virus replication. Science 2007,
315:1579-1582.
17. Grimm D, Streetz KL, Jopling CL, Storm TA, Pandey K, Davis CR,
Marion P, Salazar F, Kay MA: Fatality in mice due to oversatura-
tion of cellular microRNA/short hairpin RNA pathways.
Nature 2006, 441:537-541.
18. Lytle JR, Yario TA, Steitz JA: Target mRNAs are repressed as
efficiently by microRNA-binding sites in the 5' UTR as in the
3' UTR. Proc Natl Acad Sci USA 2007, 104:9667-9672.

19. Odadzic D, Bramsen JB, Smicius R, Bus C, Kjems J, Engels JW: Syn-
thesis of 2'-O-modified adenosine building blocks and appli-
cation for RNA interference. Bioorg Med Chem 2008, 16:518-529.
20. Abad X, Vera M, Jung SP, Oswald E, Romero I, Amin V, Fortes P,
Gunderson SI: Requirements for gene silencing mediated by
U1 snRNA binding to a target sequence. Nucleic Acids Res 2008,
36:2338-2352.
21. Bent AF, Mackey D: Elicitors, effectors, and R genes: the new
paradigm and a lifetime supply of questions. Annu Rev Phy-
topathol 2007, 45:
399-436.
22. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voin-
net O, Jones JD: A plant miRNA contributes to antibacterial
resistance by repressing auxin signaling. Science 2006,
312:436-439.
23. Navarro L, Jay F, Nomura K, He SY, Voinnet O: Suppression of the
microRNA pathway by bacterial effector proteins. Science
2008, 321:964-967.
24. Xu N, Segerman B, Zhou X, Akusjarvi G: Adenovirus virus-associ-
ated RNAII-derived small RNAs are efficiently incorporated
into the rna-induced silencing complex and associate with
polyribosomes. J Virol 2007, 81:10540-10549.
25. Grassmann R, Jeang KT: The roles of microRNAs in mammalian
virus infection. Biochim Biophys Acta 2008.
26. Ter Brake O, Legrand N, von Eije KJ, Centlivre M, Spits H, Weijer K,
Blom B, Berkhout B: Evaluation of safety and efficacy of RNAi
against HIV-1 in the human immune system (Rag-2(-/-)(c)(-/
-)) mouse model. Gene Ther 2008.
27. Judge AD, Sood V, Shaw JR, Fang D, McClintock K, Maclachlan I:
Sequence-dependent stimulation of the mammalian innate

immune response by synthetic siRNA. Nat Biotechnol 2005,
23:457-462.
28. Hornung V, Guenthner-Biller M, Bourquin C, Ablasser A, Schlee M,
Uematsu S, Noronha A, Manoharan M, Akira S, de FA, Endres S, Hart-
mann G: Sequence-specific potent induction of IFN-alpha by
short interfering RNA in plasmacytoid dendritic cells
through TLR7. Nat Med 2005, 11:263-270.
29. Aagaard L, Rossi JJ: RNAi therapeutics: principles, prospects
and challenges. Adv Drug Deliv Rev 2007, 59:75-86.